The plant ontology as a tool for comparative plant anatomy and genomic analyses

Authors: COOPER, LAUREL - Oregon State University; WALLS, RAMONA - Botanical Garden, New York; ELSER, JUSTIN - Oregon State University; GANDOLFO, MARIA - Cornell University; STEVENSON, DENNIS - Botanical Garden, New York; SMITH, BARRY - University Of Buffalo; PREECE, JUSTIN - Oregon State University; ATHREYA, BALAJI - Oregon State University; MUNGALL, CHRISTOPHER - Lawrence Berkeley National Laboratory; RENSING, STEFAN - University Of Freiburg; HISS, MANUEL - University Of Freiburg; LANG, DANIEL - University Of Freiburg; RESKI, RALF - University Of Freiburg; BERARDINI, TANYA - Carnegie Institute - Stanford; LI, DONGHUI - Carnegie Institute - Stanford; HUALA, EVA - Carnegie Institute - Stanford; Schaeffer, Mary; MENDA, NAAMA - Boyce Thompson Institute; ARNAUD, ELIZABETH - Bioversity International; SHRESTHA, ROSEMARY - International Maize & Wheat Improvement Center (CIMMYT); YAMAZAKI, YUKIKO - National Institute Of Genetics; JAISWAL, PANKAJ - Oregon State University

Submitted to: Plant Cell Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/23/2012
Publication Date: 2/1/2013
Publication URL: http://handle.nal.usda.gov/10113/57978
Citation: Cooper, L., Walls, R.L., Elser, J., Gandolfo, M.A., Stevenson, D.W., Smith, B., Preece, J., Athreya, B., Mungall, C.J., Rensing, S., Hiss, M., Lang, D., Reski, R., Berardini, T.Z., Li, D., Huala, E., Schaeffer, M.L., Menda, N., Arnaud, E., Shrestha, R., Yamazaki, Y., Jaiswal, P. 2013. The plant ontology as a tool for comparative plant anatomy and genomic analyses. Plant Cell Physiology. 54(2):1-23.

Interpretive Summary: Recent advances in sequencing and other technologies have led to a windfall of data describing plant gene compliments, the structure of the chromosomes, metabolic and protein level responses to various developmental or environmental triggers and how genes contribute to and interact to express a specific plant phnotype (property). With new species being added rapidly to the list of species whose genomes have been decoded we now have the capability to readily share the sequence data from the multitude of species within the scientific community for comparative purposes. However, data that provides functional descriptions of genes at the whole plant level is less amenable to such sharing, because the language used to describe plant anatomy and growth varies for different plants. While the biologist realizes that a maize kernel and a tomato fruit share similar functions and structures, a computer requires more instruction in order to correctly link the two. The Plant Ontology (PO) project is a publicly-available collaborative effort to share data from different species that describes gene function at the whole plant level, and in a manner compatible with the computational tools (software) that have been developed to describe gene function at the level of individual cells. From its original design covering only rice, maize, and Arabidopsis, the scope of the PO has been expanded to include all green plants, and used to describe aspects of genes and their functions in 22 different plant species, many of agronomic importance to US agriculture. In this paper, we focus on the plant anatomy and morphology branch of the PO, describe its organizing principles, the resources available to users, and examples of how the PO is integrated into many plant databases. We also provide two examples showing how the PO can be used for discovery of patterns of gene expression among species. One example is a gene family involved in development of reproductive structures. The other is a gene family important to the synthesis of a large number of biochemicals, some that are basic and required for plant growth, while others have secondary roles, such as endogenous pesticides. This project will enable plant scientists and breeeders to make rational decisions regarding the manipulation of genes through existing genetic strategies and to utilize information and knowledge gained from a wide variety of plants for specific crop improvement.

Technical Abstract: Plant science is now a major player in the fields of genomics, gene expression analysis, phenomics and metabolomics. Recent advances in sequencing technologies have led to a windfall of data, with new species being added rapidly to the list of species whose genomes have been decoded. The Plant Ontology (PO; http://www.plantontology.org/) is a publically-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy and morphology, and the stages of plant development across all green plants. The goals of the PO are to link annotated data from different species to common plant structures and stages of development, using the model adopted by the Gene Ontology. As of July 2012 there are almost 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs), covering 22 different plant species. From its original design covering only rice, maize, and Arabidopsis, the scope of the PO has been expanded to include all green plants. In this paper, we focus on the plant anatomy and morphology branch of the PO, describe its organizing principles, the resources available to users, and examples of how the PO is integrated into many other plant genomics databases and web portals. We provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LFY proteins and terpene synthase gene families.